This invention relates to an instrument that is capable of performing incubations of small volumes of reagents on the surface of a microscope slide. A variety of assays are typically carried out on the surface of a microscope slide. These assays generally aim to determine if a suspected analyte is present in a patient biopsy. They include: (1) in situ hybridization, for the detection of nucleic acid targets in a tissue or cell sample, (2) immunohistochemistry, for the detection of specific proteins in a tissue or cell sample, (3) histochemical stains, for the detection of certain types of chemical compounds or classes of microorganisms in a tissue sample. In addition, there are two other types of assays that are often carried out on the surface of a glass slide. Rather than testing for the presence of an analyte in a tissue biopsy, these assays aim to detect specific molecules in a solution. They are (1) gene arrays, whereby an array of known nucleic acid targets are immobilized directly on the glass slide, and (2) protein arrays, hereby an array of known proteins are immobilized on the glass slide.
In each of these instances, a glass slide serves as the preferred support on which the assay is carried out. The reason a glass slide is used is that it is optically clear and flat. These physical properties facilitate the ability of an instrument, such as a microscope, to optically detect a fluorescent or colorimetric signal. In order to highlight certain desired features, the above assays require that the slides be treated with a series of reagent incubations. Each incubation needs to occur for a specific time (typically 15-60 minutes) and at a specified temperature (typically, from room temperature to 95xc2x0 C.).
The optical advantages of a microscope slide are somewhat counterbalanced by certain difficulties in performing the assay. The treatment of the tissue sections on a microscope slide for the purpose of highlighting certain histologic features is often called xe2x80x9cstaining.xe2x80x9d Since the surface of the slide is flat, reagent can easily drain off the edge of the microscope slide, especially if the slide is not perfectly level. Moreover, the large surface area to volume ratio of reagent spread over the slide surface promotes evaporation. Evaporation of reagent interferes with the performance of the assay. If the reagent evaporates, then it will not continuously contact the tissue sample. Drying artifacts may cause the assay result (xe2x80x9cstainxe2x80x9d) to not be accurate. Lastly, it is important to spread the reagent over the slide surface. Surfactants are sometimes used to promote reagent spreading. If the reagent does not spread, then the reaction may fail to occur over all of the tissue biopsy, or over all portions of the array. Therefore, the prior art comprises a great number of attempts to construct apparatus and devices that aim to facilitate or automate the sample preparation/treatment steps of a biological sample on a glass slide.
The general approach to solving these problems in the past has been to enclose an area of the slide surface, forming a chamber. Desirable features for such a chamber are:
a) Liquid spreading. Reagents must be evenly spread, without entrapped air bubbles.
b) Use of minimal reagent volume (ideally less than 100 microliters to cover the slide surface).
c) Prevent evaporation when the reagent is heated to 95xc2x0 C.
d) Automatic reagent injection and removal. Namely, the apparatus needs to be compatible with an automated fluid transfer system.
e) Protection of the tissue section against physical damage.
One method of addressing at least some of the requirements described above is to entrap reagent under a coverslip. For in situ hybridization procedures, reagent is conventionally placed directly on top of the tissue section with a pipette and covered with a coverslip. The edges of the coverslip are then sealed with nail polish or rubber glue. The coverslip both spreads out the reagent into a relatively uniform layer and prevents evaporation. It is important to avoid entrapping air bubbles under the coverslip. Otherwise, there will be an area of the tissue section that does not contact the hybridization solution.
No existing technology is suited to automating coverslipping for in situ hybridization. Coverslips can be applied to slides in an automated fashion; several companies serving the histopathology market sell dedicated coverslipping machines. However, such coverslipping machines are not likely to be adaptable to this application, because (i) it will be difficult to automate sealing the coverslip edges, such as with glue, and (ii) it will be difficult to robotically remove the coverslips without damaging the tissue section.
An alternative method for spreading small amounts of reagents was described in 1988, by Unger, et.al. (Unger, E. R., D. J. Brigati, M. L. Chenggis, et.al. 1988. Automation of in situ hybridization: Application of the capillary action robotic workstation. J. Histotechnology 11:253-258.) Specifically, they described a modification of the Code-On slide stainer for use with in situ hybridization. Instead of a coverslip, two slides were placed in close apposition to each other, forming a capillary gap. Liquids, such as a hybridization solution, could then be applied to the bottom of the gap. The reagents xe2x80x9cwickedxe2x80x9d in by capillary action. Placing the slides in a heated humidity chamber prevented evaporation. The Code-On worked well in the right hands, but was labor-intensive and required a great deal of experience and care each day in setting it up. Slight scratches or imperfections in the surface of the glass slide sometimes caused air bubbles to be entrapped in the capillary gap, resulting in areas of the tissue not being stained.
An early description of a slide chamber is disclosed in U.S. Pat. Nos. 4,847,208 and 5,073,504. A chamber was apposed to the surface of a slide, forming walls capable of preventing lateral spillover of reagent. Moreover, a hinged cover minimized the evaporative loss of reagent. Each chamber included a fluid inlet and outlet port.
WO99/34190 discloses a chamber formed by the insertion of a microscope slide into a cartridge device. Reagent is dispensed onto a portion of the slide that protrudes from the cartridge and is caused to flow into a capillary gap-type space by moving the slide inwards. The chamber is not sealed from the outside environment. Therefore, reagent will be expected to evaporate, especially if the samples are heated. Moreover, reagent can flow around and underneath the slide, thereby increasing the volume requirement to cover the slide surface. Lastly, it is unclear how often bubbles will be entrapped over the slide surface, since no specific mechanism in the cartridge prevents them.
A review of other methods of forming a chamber, and their drawbacks, are also described in the Background section of WO99/34190.
In embodiments of the present invention, a fluid handling apparatus is capable of spreading small amounts of liquid reagent over a flat surface, such as a microscope glass slide. The reagent may be sealed within a confined cavity, or xe2x80x9cchamberxe2x80x9d, so as to prevent evaporation even with heating of small amounts of reagent during an incubation period. One surface of this chamber is the flat slide surface. The remaining surfaces are formed by a cell. The cell is preferably a plastic disposable part that fits on top of the slide, over the area containing the tissue, biologic cells, or array mounted on the glass slide. The cell forms a fluid seal to the surface of the glass by means of a gasket. The gasket is mounted in a recess on the face of the cell that mates with the glass slide.
Each cell has two fluid ports. These ports are in fluid communication with the chamber. Therefore, when liquid reagent is inserted into a fluid port, it can travel into the chamber and contact the biologic sample or array mounted on the glass surface. The fluid ports on a cell are preferably positioned on opposite ends of the cell. This allows for liquid reagent or wash solution to flow in one fluid port, fill the chamber, and then exit the other fluid port at the other end of the cell. Each fluid port has a valve occluding the orifice that is normally closed. Consequently, the chamber is sealed. Unless the valves are opened, the chamber is normally not accessible to the outside environment. Liquid reagents or wash solutions are only added or removed by opening one or both of the valves associated with the fluid ports. The fact that the fluid ports are normally sealed by valves helps prevent evaporation.
The instrument comprises a plurality of positions for glass slides. Each position has a mechanism to clamp a cell to the glass slide. Keeping the cell and slide apposed to each other in a fixed spatial relationship is important in forming a sealed chamber for reagent incubations. Reagents and wash solutions are added and removed by the use of two liquid handling xe2x80x9cstationsxe2x80x9d. In the illustrated embodiment, the liquid handling stations move over non-moving slides. It is also conceivable, and ultimately preferred in an automated instrument, to reverse that relationship to automate the staining process by moving the slides, such as on a rotary carousel. The slides would move past non-moving liquid handling stations positioned on the periphery of the rotary carousel of slides. This type of arrangement is described in U.S. Pat. No. 5,947,167 by the same inventors which is incorporated by reference in its entirety.
The method of adding and subsequently washing reagents out from the chamber is an important part of this system. Washing reagent out from the chamber is required after an incubation, to thoroughly remove any unreacted reagent before the subsequent treatment step. Washing usually involves treating the biologic sample mounted on the glass slide with an excess of a buffer or wash solution. The unreacted reagent is diluted in the excess volume of the wash solution and removed by aspirating away the wash solution. In this system, washing the biologic sample involves flushing the chamber containing the biologic sample with the wash solution. Wash solution is pumped in one fluid port and removed from the other. This process requires the presence of a xe2x80x9cfluid injectorxe2x80x9d and a xe2x80x9cfluid aspiratorxe2x80x9d, each articulating with a fluid port. Each injector or aspirator has a piston that is capable of opening the valve positioned in the fluid port. The piston opens the valve by deflecting an elastomeric seal that occludes the orifice of the fluid port. For the purpose of washing the biologic sample, a fluid injector pushes wash solution into the chamber. The fluid aspirator captures the reagent after it has passed through the chamber. The fluid aspirator can then channel the waste wash fluid to one or more reservoirs for ultimate disposal. This washing process occurs at a xe2x80x9cwash stationxe2x80x9d that has one fluid injector and one fluid aspirator. The injector and aspirator are mounted on to a mechanism that lowers and raises them together.
Reagent injection into the chamber occurs at a separate xe2x80x9creagent injection stationxe2x80x9d. Two different methods for injecting reagent will be described. The first step for both methods is that a small aliquot of the desired reagent to be injected is placed in a reagent well at the fluid inlet port. In the first method, the reagent injection station includes only a fluid injector. The fluid injector is mounted on to a mechanism that lowers the injector so that the injector articulates with the fluid port on the cell. As the fluid injector is lowered, it first forms a fluid-tight seal to the fluid port. The piston on the injector then opens the valve in the fluid port. A strong momentary vacuum is then drawn through the fluid injector. The vacuum is transmitted through the fluid port into the chamber. The small amount of air in the chamber bubbles up through the reagent in the reagent well. The vacuum in the fluid injector is then released, returning the pressure above the reagent to atmospheric level. The reagent is then drawn into the chamber by the strong residual vacuum in the chamber. Bubbles do not form because there is little to no air in the chamber to form an air bubble. Alternatively, the vacuum can be drawn through a second port which is closed before the port to the aliquot is opened. In either approach, the liquid is drawn into but not through the chamber by the vacuum.
In another method of fluid injection, reagent is placed into the reagent well, as before. A fluid injector is positioned above the fluid inlet port. In addition, the fluid aspirator is positioned above the fluid outlet port. The valves of both fluid ports are opened by this process. Reagent is then pushed into the chamber by a burst of air pressure. The transient, high-pressure reagent injection avoids entrapping bubbles by forcing laminar flow of reagent through the chamber. Once the reagent completely fills the chamber, the pressure is removed and the valves are closed by disengaging the fluid injector and fluid aspirator.
Thus, in accordance with one aspect of the invention, an apparatus for adding and removing liquid reagents to and from a sample comprises a flat surface supporting the sample and a chamber forming a cavity on the flat surface, the chamber being releasably sealed to the flat surface. Fluids can be added or removed through a fluid port in the wall of the chamber. A source of negative or positive air pressure is provided in a conduit, and an actuator is able to move the fluid port and conduit relative to each other to engage the conduit and fluid ports to each other so that the two are in fluid communication.
The chamber may include a valve that is positioned at the fluid port, and the conduit may further include a piston capable of opening the valve when the conduit and port are in communication with each other. A preferred valve is a flexible element below the port which is an extension of a gasket of the chamber which seals against the flat surface.
A well capable of holding an aliquot of reagent may be provided over the fluid port. Multiple chambers may be moved relative to the actuator to position a selected chamber at the actuator.
Another aspect of the invention includes novel methods of applying reagent to a sample. In one method, a vacuum is applied to the chamber in which the sample is positioned. After application of the vacuum ceases, the reagent is allowed to be drawn into the chamber by the vacuum formed within the chamber. In a preferred approach, the vacuum is applied to the chamber through an aliquot of reagent held in a well. When application of the vacuum above the aliquot ceases, the aliquot is drawn into the chamber.
In accordance with another novel method, a sealed chamber is apposed to a flat surface supporting the sample. An aliquot of reagent is dispensed into a reagent well located above a fluid port in the chamber. A source of air pressure is applied to the fluid port to cause the reagent to be pushed through the fluid port into the chamber.